Zheng, C. et al. Panorama of infiltrating T cells in liver most cancers revealed by single-cell sequencing. Cell 169, 1342–1356.e1316 (2017).
Azizi, E. et al. Single-cell map of various immune phenotypes within the breast tumor microenvironment. Cell 174, 1293–1308.e1236 (2018).
Simoni, Y. et al. Bystander CD8+ T cells are considerable and phenotypically distinct in human tumour infiltrates. Nature 557, 575–579 (2018).
Zhang, L. et al. Lineage monitoring reveals dynamic relationships of T cells in colorectal most cancers. Nature 564, 268–272 (2018).
Zheng, L. et al. Pan-cancer single-cell panorama of tumor-infiltrating T cells. Science 374, abe6474 (2021).
Schumacher, T. N. & Schreiber, R. D. Neoantigens in most cancers immunotherapy. Science 348, 69–74 (2015).
Yarchoan, M., Hopkins, A. & Jaffee, E. M. Tumor mutational burden and response fee to PD-1 inhibition. New Engl. J. Med. 377, 2500–2501 (2017).
Dadi, S. et al. Most cancers immunosurveillance by tissue-resident innate lymphoid cells and innate-like T cells. Cell 164, 365–377 (2016).
DuPage, M., Mazumdar, C., Schmidt, L. M., Cheung, A. F. & Jacks, T. Expression of tumour-specific antigens underlies most cancers immunoediting. Nature 482, 405–409 (2012).
Matsushita, H. et al. Most cancers exome evaluation reveals a T-cell-dependent mechanism of most cancers immunoediting. Nature 482, 400–404 (2012).
Chen, D. S. & Mellman, I. Components of most cancers immunity and the cancer-immune set level. Nature 541, 321–330 (2017).
McLane, L. M., Abdel-Hakeem, M. S. & Wherry, E. J. CD8 T cell exhaustion throughout persistent viral an infection and most cancers. Annu. Rev. Immunol. 37, 457–495 (2019).
Sharma, P. & Allison, J. P. The way forward for immune checkpoint remedy. Science 348, 56–61 (2015).
Topalian, S. L., Taube, J. M., Anders, R. A. & Pardoll, D. M. Mechanism-driven biomarkers to information immune checkpoint blockade in most cancers remedy. Nat. Rev. Most cancers 16, 275–287 (2016).
Baumeister, S. H., Freeman, G. J., Dranoff, G. & Sharpe, A. H. Coinhibitory pathways in immunotherapy for most cancers. Annu. Rev. Immunol. 34, 539–573 (2016).
Schneider, W. M., Chevillotte, M. D. & Rice, C. M. Interferon-stimulated genes: a fancy net of host defenses. Annu. Rev. Immunol. 32, 513–545 (2014).
Yost, Ok. E. et al. Clonal substitute of tumor-specific T cells following PD-1 blockade. Nat. Med. 25, 1251–1259 (2019).
Savage, P. A. et al. Recognition of a ubiquitous self antigen by prostate cancer-infiltrating CD8+ T lymphocytes. Science 319, 215–220 (2008).
Ise, W. et al. CTLA-4 suppresses the pathogenicity of self antigen-specific T cells by cell-intrinsic and cell-extrinsic mechanisms. Nat. Immunol. 11, 129–135 (2010).
Hildner, Ok. et al. Batf3 deficiency reveals a essential function for CD8α+ dendritic cells in cytotoxic T cell immunity. Science 322, 1097–1100 (2008).
Starr, T. Ok., Jameson, S. C. & Hogquist, Ok. A. Optimistic and adverse choice of T cells. Annu. Rev. Immunol. 21, 139–176 (2003).
Eberl, G. & Littman, D. R. Thymic origin of intestinal αβ T cells revealed by destiny mapping of RORγ+ cells. Science 305, 248–251 (2004).
Georgiev, H., Peng, C., Huggins, M. A., Jameson, S. C. & Hogquist, Ok. A. Classical MHC expression by DP thymocytes impairs the choice of non-classical MHC restricted innate-like T cells. Nat. Commun. 12, 2308 (2021).
Stritesky, G. L., Jameson, S. C. & Hogquist, Ok. A. Choice of self-reactive T cells within the thymus. Annu. Rev. Immunol. 30, 95–114 (2012).
Ruscher, R., Kummer, R. L., Lee, Y. J., Jameson, S. C. & Hogquist, Ok. A. CD8αα intraepithelial lymphocytes come up from two fundamental thymic precursors. Nat. Immunol. 18, 771–779 (2017).
Gazit, R. et al. Fgd5 identifies hematopoietic stem cells within the murine bone marrow. J. Exp. Med. 211, 1315–1331 (2014).
Ruscher, R. et al. Intestinal CD8αα IELs derived from two distinct thymic precursors have staggered ontogeny. J. Exp. Med. 217, e20192336 (2020).
Khan, O. et al. TOX transcriptionally and epigenetically packages CD8+ T cell exhaustion. Nature 571, 211–218 (2019).
Alfei, F. et al. TOX reinforces the phenotype and longevity of exhausted T cells in persistent viral an infection. Nature 571, 265–269 (2019).
Scott, A. C. et al. TOX is a essential regulator of tumour-specific T cell differentiation. Nature 571, 270–274 (2019).
Chinen, T. et al. A vital function for the IL-2 receptor in Treg cell perform. Nat. Immunol. 17, 1322–1333 (2016).
Correia, M. P. et al. Distinct human circulating NKp30+FcεRIγ+CD8+ T cell inhabitants exhibiting excessive pure killer-like antitumor potential. Proc. Natl Acad. Sci. USA 115, E5980–E5989 (2018).
Perarnau, B. et al. Single H2Kb, H2Db and double H2KbDb knockout mice: peripheral CD8+ T cell repertoire and anti-lymphocytic choriomeningitis virus cytolytic responses. Eur. J. Immunol. 29, 1243–1252 (1999).
Sosinowski, T. et al. CD8α+ dendritic cell trans presentation of IL-15 to naive CD8+ T cells produces antigen-inexperienced T cells within the periphery with reminiscence phenotype and performance. J. Immunol. 190, 1936–1947 (2013).
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic knowledge throughout totally different situations, applied sciences, and species. Nat. Biotechnol. 36, 411–420 (2018).
Stuart, T. et al. Complete integration of single-cell knowledge. Cell 177, 1888–1902.e1821 (2019).
Angerer, P. et al. future: diffusion maps for large-scale single-cell knowledge in R. Bioinformatics 32, 1241–1243 (2016).
Haghverdi, L., Buettner, F. & Theis, F. J. Diffusion maps for high-dimensional single-cell evaluation of differentiation knowledge. Bioinformatics 31, 2989–2998 (2015).
Trapnell, C. et al. The dynamics and regulators of cell destiny selections are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).
Qiu, X. et al. Single-cell mRNA quantification and differential evaluation with Census. Nat. Strategies 14, 309–315 (2017).
Qiu, X. et al. Reversed graph embedding resolves advanced single-cell trajectories. Nat. Strategies 14, 979–982 (2017).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a quick spliced aligner with low reminiscence necessities. Nat. Strategies 12, 357–360 (2015).
Mudge, J. M. & Harrow, J. Creating reference gene annotation for the mouse C57BL6/J genome meeting. Mamm. Genome 26, 366–378 (2015).
Liao, Y., Smyth, G. Ok. & Shi, W. The Subread aligner: quick, correct and scalable learn mapping by seed-and-vote. Nucleic Acids Res. 41, e108 (2013).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq knowledge with DESeq2. Genome Biol. 15, 550 (2014).
Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package deal for evaluating organic themes amongst gene clusters. OMICS 16, 284–287 (2012).
Yang, Y. et al. Distinct mechanisms outline murine B cell lineage immunoglobulin heavy chain (IgH) repertoires. eLife 4, e09083 (2015).
Wang, C. et al. Excessive-throughput, high-fidelity HLA genotyping with deep sequencing. Proc. Natl Acad. Sci. USA 109, 8676–8681 (2012).
Lefranc, M. P. et al. IMGT, the worldwide ImMunoGeneTics database. Nucleic Acids Res. 27, 209–212 (1999).
Franklin, R. A. et al. The mobile and molecular origin of tumor-associated macrophages. Science 344, 921–925 (2014).
Gasteiger, G., Fan, X., Dikiy, S., Lee, S. Y. & Rudensky, A. Y. Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs. Science 350, 981–985 (2015).
Morita, S., Kojima, T. & Kitamura, T. Plat-E: an environment friendly and steady system for transient packaging of retroviruses. Gene Ther. 7, 1063–1066 (2000).
Sanjana, N. E., Shalem, O. & Zhang, F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Strategies 11, 783–784 (2014).
Mayans, S. et al. αβT cell receptors expressed by CD4−CD8 αβ intraepithelial T cells drive their destiny into a singular lineage with uncommon MHC reactivities. Immunity 41, 207–218 (2014).
McDonald, B. D., Bunker, J. J., Ishizuka, I. E., Jabri, B. & Bendelac, A. Elevated T cell receptor signaling identifies a thymic precursor to the TCR αβ+CD4−CD8β− intraepithelial lymphocyte lineage. Immunity 41, 219–229 (2014).
Constantinides, M. G., McDonald, B. D., Verhoef, P. A. & Bendelac, A. A dedicated precursor to innate lymphoid cells. Nature 508, 397–401 (2014).